bims-skolko Biomed News
on Scholarly communication
Issue of 2022‒07‒03
seventeen papers selected by
Thomas Krichel
Open Library Society
  1. Publishing clinical prActice GuidelinEs (PAGE): Recommendations from editors and reviewers.
  2. Statistical inference through estimation: recommendations from the International Society of Physiotherapy Journal Editors.
  3. Data privacy protection in scientific publications: process implementation at a pharmaceutical company.
  4. Silence greets requests to flag retracted studies.
  5. Peer review journals publishing surveys of Chinese views on government pandemic performance: Invalid science and ethically wrong.
  6. Excellence in peer-review: The hallmark and fundamental of a good society-owned journal.
  7. What the American Journal of Critical Care Junior Peer Reviewers Were Reading During the First Year of the Program: Caring for Patients With COVID-19.
  8. Recommendations to medical journals on ways to encourage statistical experts to review submissions.
  9. Reporting Quality in Abstracts of Randomized Controlled Trials Published in High-Impact Occupational Therapy Journals.
  10. Establishing Institutional Scores With the Rigor and Transparency Index: Large-scale Analysis of Scientific Reporting Quality.
  11. [Presumed guilty. Falsification and fabrication of data in scientific publications.]
  12. Inequity in Peer Review in Communication Sciences and Disorders.
  13. Effectiveness of a manuscript writing workshop on writing confidence amongst nursing and health disciplines clinicians.
  14. An open chat with…Alexander Wlodawer.
  15. JGME Invites Visual Abstracts for Accepted Research Papers.
  16. Scientific papers: the sum of the parts is greater than the whole.
  17. Living and publishing in the era of the COVID-19 pandemic.
  1. J Evid Based Med. 2022 Jun 29.
    Publishing clinical prActice GuidelinEs (PAGE): Recommendations from editors and reviewers.
    TERM Working Group
      Transparency Ecosystem for Research and Journals in Medicine (TERM) Working Group summarized the essential recommendations that should be considered to review and publish a high-quality guideline. These recommendations from editors and reviewers included the ten components of essential requirements: systematic review of existing relevant guidelines, guideline registration, guideline protocol, stakeholders, conflicts of interest, clinical questions, systematic reviews, recommendation consensus, guideline reporting, and external review. TERM Working Group abbreviates them as PAGE (essential requirements for Publishing clinical prActice GuidelinEs), recommends guideline authors, editors, and peer reviewers use them for high-quality guidelines.
    Keywords:  editor; guidelines; peer review; recommendations
    DOI:  https://doi.org/10.1111/jebm.12479
  2. J Man Manip Ther. 2022 Jun;30(3): 133-138
    Statistical inference through estimation: recommendations from the International Society of Physiotherapy Journal Editors.
    Mark R Elkins, Rafael Zambelli Pinto, Arianne Verhagen, Monika Grygorowicz, Anne Söderlund, Matthieu Guemann, Antonia Gómez-Conesa, Sarah Blanton, Jean-Michel Brismée, Shabnam Agarwal, Alan Jette, Sven Karstens, Michele Harms, Geert Verheyden, Umer Sheikh.
      
    DOI:  https://doi.org/10.1080/10669817.2022.2071980
  3. BMC Med Ethics. 2022 Jun 25. 23(1): 65
    Data privacy protection in scientific publications: process implementation at a pharmaceutical company.
    Friedrich Maritsch, Ingeborg Cil, Colin McKinnon, Jesse Potash, Nicole Baumgartner, Valérie Philippon, Borislava G Pavlova.
      BACKGROUND: Sharing anonymized/de-identified clinical trial data and publishing research outcomes in scientific journals, or presenting them at conferences, is key to data-driven scientific exchange. However, when data from scientific publications are linked to other publicly available personal information, the risk of reidentification of trial participants increases, raising privacy concerns. Therefore, we defined a set of criteria allowing us to determine and minimize the risk of data reidentification. We also implemented a review process at Takeda for clinical publications prior to submission for publication in journals or presentation at medical conferences.METHODS: Abstracts, manuscripts, posters, and oral presentations containing study participant information were reviewed and the potential impact on study participant privacy was assessed. Our focus was on direct (participant ID, initials) and indirect identifiers, such as sex, age or geographical indicators in rare disease studies or studies with small sample size treatment groups. Risk minimization was sought using a generalized presentation of identifier-relevant information and decision-making on data sharing for further research. Additional risk identification was performed based on study participant/personnel parameters present in materials destined for the public domain. The potential for participant/personnel identification was then calculated to facilitate presentation of meaningful but de-identified information.
    RESULTS: The potential for reidentification was calculated using a risk ratio of the exposed versus available individuals, with a value above the threshold of 0.09 deemed an unacceptable level of reidentification risk. We found that in 13% of Takeda clinical trial publications reviewed, either individuals could potentially be reidentified (despite the use of anonymized data sets) or inappropriate data sharing plans could pose a data privacy risk to study participants. In 1/110 abstracts, 58/275 manuscripts, 5/87 posters and 3/58 presentations, changes were necessary due to data privacy concerns/rules. Despite the implementation of risk-minimization measures prior to release, direct and indirect identifiers were found in 11% and 34% of the analysed documents, respectively.
    CONCLUSIONS: Risk minimization using de-identification of clinical trial data presented in scientific publications and controlled data sharing conditions improved privacy protection for study participants. Our results also suggest that additional safeguards should be implemented to ensure that higher data privacy standards are met.
    Keywords:  Clinical trials; Data de‑identification; Data sharing; Medical publications; Patient privacy; Reidentification risk; Trial participant privacy
    DOI:  https://doi.org/10.1186/s12910-022-00804-w
  4. Science. 2022 Jul;377(6601): 11-12
    Silence greets requests to flag retracted studies.
    Jeffrey Brainard.
      Authors and editors ignored warnings about citing noted fraudster, exposing a problem in scholarly publishing.
    DOI:  https://doi.org/10.1126/science.add6988
  5. Ethics Med Public Health. 2022 Aug;23 100808
    Peer review journals publishing surveys of Chinese views on government pandemic performance: Invalid science and ethically wrong.
    G A Gellert.
      
    Keywords:  China government pandemic control; Chinese pandemic attitudes
    DOI:  https://doi.org/10.1016/j.jemep.2022.100808
  6. J Neuroendocrinol. 2022 Jun 04. e13173
    Excellence in peer-review: The hallmark and fundamental of a good society-owned journal.
    Julian G Mercer.
      At the RegPep23 meeting organised by the International Regulatory Peptides Society (IRPS) in August 2021, in-person and online delegates had the opportunity to engage in and contribute to "an exploration of how our scientific community can support the journals that truly fulfil the mission of advancing science communication for all scientists". The Theme X session was entitled "Scientific publishing: obligations and opportunities". The lead discussants were Julian Mercer, Bob Millar, Dave Grattan, and Gareth Leng, current and past Editors-in-Chief of Journal of Neuroendocrinology, the IRPS official journal; Willis (Rick) Samson, former Editor-in-Chief, American Journal of Physiology - Regulatory, Integrative, and Comparative Physiology, and Deputy Editor-in-Chief, Physiological Reviews; and Lee Eiden, IRPS Co-President. The full transcript of this discussion from RegPep23 is available at http://www.regpep.org/, with a summary of the key points in the text box below.
    DOI:  https://doi.org/10.1111/jne.13173
  7. Am J Crit Care. 2022 Jul 01. 31(4): e26-e30
    What the American Journal of Critical Care Junior Peer Reviewers Were Reading During the First Year of the Program: Caring for Patients With COVID-19.
    L Douglas Smith, Jennifer Berube, Mintie Indar-Maraj, Patricia Rosier, Janeane Walker, Christian Justin Carreon, Regi Freeman, Katie Gabel, Angelica Hernandez, Meghan Kolmer, Tamala Proctor, Aluko A Hope.
      The Junior Peer Reviewer program of the American Journal of Critical Care provides mentorship in the peer review process to novice reviewers. The program includes discussion sessions in which participants review articles published in other journals to practice and improve their critical appraisal skills. The articles reviewed during the first year of the program focused on caring for patients with COVID-19. The global pandemic has placed a heavy burden on nursing practice. Prone positioning of patients with acute respiratory failure is likely to improve their outcomes. Hospitals caring for patients needing prolonged ventilation should use evidence-based, standardized care practices to reduce mortality. The burden on uncompensated caregivers of COVID-19 survivors is also high, and such caregivers are likely to require assistance with their efforts. Reviewing these articles was helpful for building the peer review skills of program participants and identifying actionable research to improve the lives of critically ill patients.
    DOI:  https://doi.org/10.4037/ajcc2022158
  8. Curr Med Res Opin. 2022 Jun 30. 1-3
    Recommendations to medical journals on ways to encourage statistical experts to review submissions.
    Michal Ordak.
      
    Keywords:  Biostatistics; Medicine; Statistical reviews
    DOI:  https://doi.org/10.1080/03007995.2022.2096335
  9. Am J Occup Ther. 2022 Jul 01. pii: 7604205120. [Epub ahead of print]76(4):
    Reporting Quality in Abstracts of Randomized Controlled Trials Published in High-Impact Occupational Therapy Journals.
    Paula Fernández-Pires, Daniel Prieto-Botella, Desirée Valera-Gran, Miriam Hurtado-Pomares, Cristina Espinosa-Sempere, Alicia Sánchez-Pérez, Iris Juárez-Leal, Paula Peral-Gómez, Leticia Moreno-Campos, Eva-María Navarrete-Muñoz.
      IMPORTANCE: Adequate reporting in the abstracts of randomized controlled trials (RCTs) is essential to enable occupational therapy practitioners to critically appraise the validity of findings.OBJECTIVE: To evaluate the reporting quality and characteristics of RCT abstracts published between 2008 and 2018 in the occupational therapy journals with the five highest impact factors in 2018.
    DESIGN: A descriptive cross-sectional study.
    DATA SOURCES: The American Journal of Occupational Therapy (AJOT), Australian Occupational Therapy Journal (AOTJ), Canadian Journal of Occupational Therapy (CJOT), Scandinavian Journal of Occupational Therapy (SJOT), and Physical and Occupational Therapy in Pediatrics (POTP) were identified using a Web of Science search.
    STUDY SELECTION AND DATA COLLECTION: We searched Scopus for abstracts in the five included journals. We used a 17-point scale based on the CONSORT for Abstracts (CONSORT-A) checklist to assess reporting quality. We also identified characteristics of the abstracts.
    FINDINGS: Seventy-eight RCT abstracts were assessed and showed moderate to low adherence to the CONSORT-A checklist (Mdn = 8, interquartile range = 7-9). Abstracts of articles with authors from a higher number of institutions, European first authors, and >200 words had higher CONSORT-A scores. The most underreported CONSORT-A items were trial design, blinding, numbers analyzed, outcome (results), harms, trial registration, and funding.
    CONCLUSIONS AND RELEVANCE: Between 2008 and 2018, the reporting quality in RCT abstracts from the five highest impact occupational therapy journals was moderate to low. Inadequate reporting in RCT abstracts raises the risk that occupational therapy practitioners will make ineffective clinical decisions based on misinterpretation of findings. What This Article Adds: Reporting quality in RCT abstracts in occupational therapy journals is moderate to low. Journal editors should require authors of RCTs to use the CONSORT-A checklist to promote optimal reporting and transparency in abstracts.
    DOI:  https://doi.org/10.5014/ajot.2022.042333
  10. J Med Internet Res. 2022 Jun 27. 24(6): e37324
    Establishing Institutional Scores With the Rigor and Transparency Index: Large-scale Analysis of Scientific Reporting Quality.
    Joe Menke, Peter Eckmann, Ibrahim Burak Ozyurt, Martijn Roelandse, Nathan Anderson, Jeffrey Grethe, Anthony Gamst, Anita Bandrowski.
      BACKGROUND: Improving rigor and transparency measures should lead to improvements in reproducibility across the scientific literature; however, the assessment of measures of transparency tends to be very difficult if performed manually.OBJECTIVE: This study addresses the enhancement of the Rigor and Transparency Index (RTI, version 2.0), which attempts to automatically assess the rigor and transparency of journals, institutions, and countries using manuscripts scored on criteria found in reproducibility guidelines (eg, Materials Design, Analysis, and Reporting checklist criteria).
    METHODS: The RTI tracks 27 entity types using natural language processing techniques such as Bidirectional Long Short-term Memory Conditional Random Field-based models and regular expressions; this allowed us to assess over 2 million papers accessed through PubMed Central.
    RESULTS: Between 1997 and 2020 (where data were readily available in our data set), rigor and transparency measures showed general improvement (RTI 2.29 to 4.13), suggesting that authors are taking the need for improved reporting seriously. The top-scoring journals in 2020 were the Journal of Neurochemistry (6.23), British Journal of Pharmacology (6.07), and Nature Neuroscience (5.93). We extracted the institution and country of origin from the author affiliations to expand our analysis beyond journals. Among institutions publishing >1000 papers in 2020 (in the PubMed Central open access set), Capital Medical University (4.75), Yonsei University (4.58), and University of Copenhagen (4.53) were the top performers in terms of RTI. In country-level performance, we found that Ethiopia and Norway consistently topped the RTI charts of countries with 100 or more papers per year. In addition, we tested our assumption that the RTI may serve as a reliable proxy for scientific replicability (ie, a high RTI represents papers containing sufficient information for replication efforts). Using work by the Reproducibility Project: Cancer Biology, we determined that replication papers (RTI 7.61, SD 0.78) scored significantly higher (P<.001) than the original papers (RTI 3.39, SD 1.12), which according to the project required additional information from authors to begin replication efforts.
    CONCLUSIONS: These results align with our view that RTI may serve as a reliable proxy for scientific replicability. Unfortunately, RTI measures for journals, institutions, and countries fall short of the replicated paper average. If we consider the RTI of these replication studies as a target for future manuscripts, more work will be needed to ensure that the average manuscript contains sufficient information for replication attempts.
    Keywords:  cell line authentication; data and code availability; reporting transparency; reproducibility crisis; research metric; research reproducibility; rigor and transparency; science of science; university ranking
    DOI:  https://doi.org/10.2196/37324
  11. Recenti Prog Med. 2022 Jun;113(6): 353-354
    [Presumed guilty. Falsification and fabrication of data in scientific publications.]
    Luca De Fiore, Antonio Addis.
      The falsification of results and the fabrication of scientific research data are on the rise. Famous researchers see their articles pulled from leading journals. Often, however, this editorial malpractice does not harm the reputation of the authors, who continue to progress in their careers. The solution cannot come from a greater awareness of researchers, sponsors, regulatory agencies or research institutions: the incentives for malpractice are too strong. We need a new international governance of research and communication.
    DOI:  https://doi.org/10.1701/3827.38106
  12. Am J Speech Lang Pathol. 2022 Jun 27. 1-15
    Inequity in Peer Review in Communication Sciences and Disorders.
    Teresa M Girolamo, Nichol Castro, Danai Kasambira Fannin, Samantha Ghali, Kerry Mandulak.
      PURPOSE: The American Speech-Language-Hearing Association (ASHA) has committed to advancing diversity, equity, and inclusion (DEI) by retaining and advancing Black, Indigenous, and people of color (BIPOC) individuals in the discipline of communication sciences and disorders (CSD), amid critical shortages of faculty to train the next generation of practitioners and researchers. Publishing research is central to the recruitment, retention, and advancement of faculty. However, inequity in peer review may systematically target BIPOC scholars, adding yet another barrier to their success as faculty. This viewpoint article addresses the challenge of inequity in peer review and provides some practical strategies for developing equitable peer-review practices. First, we describe the demographics of ASHA constituents, including those holding research doctorates, who would typically be involved in peer review. Next, we explore the peer-review process, describing how inequity in peer review may adversely impact BIPOC authors or research with BIPOC communities. Finally, we offer real-world examples of and a framework for equitable peer review.CONCLUSIONS: Inequity at the individual and systemic levels in peer review can harm BIPOC CSD authors. Such inequity has effects not limited to peer review itself and exerts long-term adverse effects on the recruitment, retention, and advancement of BIPOC faculty in CSD. To uphold ASHA's commitment to DEI and to move the discipline of CSD forward, it is imperative to build equity into the editorial structure for publishing, the composition of editorial boards, and journals content. While we focus on inequity in CSD, these issues are relevant to other disciplines.
    DOI:  https://doi.org/10.1044/2022_AJSLP-21-00252
  13. J Med Imaging Radiat Sci. 2022 Jun 23. pii: S1939-8654(22)00286-7. [Epub ahead of print]
    Effectiveness of a manuscript writing workshop on writing confidence amongst nursing and health disciplines clinicians.
    Daniela Bellicoso, Teresa J Valenzano, Jane Topolovec-Vranic.
      BACKGROUND: Dissemination of practice-based research findings is critical to advancing evidence and improving practice. While frontline clinicians are well-positioned to identify gaps in practice-based evidence, many barriers exist that challenge their ability to write and submit manuscripts for publication.PURPOSE: Our study examined whether a manuscript writing workshop effectively increased nursing and health discipline clinicians' self-perceived confidence in manuscript writing.
    METHOD: Participants recruited from an ongoing manuscript writing workshop completed an assessment tool at the beginning and end of each session. Thirty-one assessment tools were completed.
    RESULTS: Participants reported higher levels of confidence following participation in the manuscript writing sessions. They also noted high levels of satisfaction with the session.
    CONCLUSIONS: A manuscript writing workshop providing a supportive environment, mentorship, protected time, and quiet space is an effective way for leadership to increase confidence in manuscript writing amongst nursing and health disciplines clinicians.
    Keywords:  Clinician focused education; Confidence; Health disciplines; Manuscript writing; Nursing
    DOI:  https://doi.org/10.1016/j.jmir.2022.06.002
  14. FEBS Open Bio. 2022 Jul 02.
    An open chat with…Alexander Wlodawer.
    Ioannis Tsagakis, Alexander Wlodawer.
      Alexander Wlodawer has been a member of the FEBS Open Bio Editorial Board since the journal's launch in 2011. Currently, he is Senior Investigator at the Center for Structural Biology, National Cancer Institute in Frederick, Maryland, USA. He received his Ph.D. from the University of California, Los Angeles in 1974, completed postdoctoral training at Stanford University and has also worked at the National Bureau of Standards, the ABL-Basic Research Program at the NCI-FCRDC and the University of Cambridge, UK. He is Doctor Honoris Causa of the Technical University of Lodz, Poland. Alexander Wlodawer is also a recipient of the 2006 NCI Mentor of Merit Award, was awarded the Heyrovsky Honorary Medal by the Czech Academy of Sciences in 2008, was elected Foreign Member of the Polish Academy of Sciences in 2005, and has been member of the Editorial Board of The FEBS Journal since 2007. He is currently Editor-in-Chief of the journal Current Research in Structural Biology. Here, Alexander Wlodawer shares with us his experiences on solving the structures of IL-4 and retroviral proteases, advice on how to deal with being scooped, and his thoughts on the importance of open data sharing and the future of AlphaFold.
    DOI:  https://doi.org/10.1002/2211-5463.13462
  15. J Grad Med Educ. 2022 06;14(3): 254-255
    JGME Invites Visual Abstracts for Accepted Research Papers.
    Gail M Sullivan, Kenneth Warren Foster, Deborah Simpson.
      
    DOI:  https://doi.org/10.4300/JGME-D-22-00349.1
  16. Clin Exp Optom. 2022 Jul;105(5): 457-458
    Scientific papers: the sum of the parts is greater than the whole.
    Nathan Efron, Philip B Morgan.
      
    DOI:  https://doi.org/10.1080/08164622.2022.2075254
  17. Korean J Transplant. 2020 Sep 30. 34(3): 133
    Living and publishing in the era of the COVID-19 pandemic.
    Ik Jin Yun.
      
    DOI:  https://doi.org/10.4285/kjt.2020.34.3.133
This page is being maintained by Thomas Krichel. It was last updated on 2022‒07‒04 at 12:48:52.